Matthew Junker, Ph.D.

   Assistant Professor of Chemistry

   Faculty Advisor, Biochemistry Program

   Department of Physical Sciences • Program in Chemistry

   Kutztown University

   314 Boehm Science Center            FAX:  (610) 683-1352

   Phone:  (610) 683-4199                    Email:  junker@kutztown.edu

   CHM 310, CHM 311        Biochemistry I with laboratory         lecture syllabus     lab syllabus

   CHM 312, CHM 313        Biochemistry II with laboratory        lecture syllabus     lab syllabus

   CHM 215                        Organic Chemistry I laboratory

   CHM 217                        Organic Chemistry II laboratory

   CHM 318                        Advanced Biochemistry (Protein Structure & Function)

   CHM 370, 371                 Research in Chemistry

Course materials available online at Blackboard

Current student researchers:  Haley Andersen, Drew Tietz

Prior KU student researchers:  James Bowalick, Lindy Carpenter, Ethan Daniels,

Marcela Ferreira, Kevin Frey, Kyle Webb

Overview

Many cellular processes are carried out by proteins, tiny machines that catalyze chemical reactions, transport molecules within and between cells, provide cell architecture, and regulate gene expression and cell growth.  The ability of proteins to carry out specific processes depends on their structure and energetics: active site geometries, complementation of recognition surfaces, conformational changes, affinities, stability of folds.  In this laboratory, we investigate the molecular mechanism of proteins that function in programmed cell death, gene expression, and bacterial pathogenesis. 

Experimental approach

All projects generally follow a common set of steps:

   1.  Use recombinant DNA methods (cloning) to insert into bacteria the genes for proteins of interest.

   2.  Grow bacteria to make the proteins of interest.

   3.  Lyse (break open) the bacteria and purify the proteins of interest.

   4.  Carry out complementary functional (biochemical assays) and structural studies of the purified proteins. 

Example: Studies of apoptosis

Apoptosis (programmed cell death) is a process in all animals that eliminates unneeded or unhealthy cells, such as aged cells that need to be regenerated or cells that are at risk for causing cancer.  Dysfunction in apoptosis can lead to cancer or neurodegenerative diseases.  At a biochemical level, apoptosis requires the activation of caspase enzymes.  Caspases are normally held in check by the Inhibitor of Apoptosis (IAP) proteins.  Certain apoptosis stimulators bind to IAPs to de-inhibit (activate) caspases. 

Studies in living cells had shown that alteration of a highly conserved Arg amino acid in IAPs caused dysfunction in apoptosis.  Using purified proteins and a protein binding assay, this laboratory showed that the dysfunction resulted from a loss in the ability of the IAP to bind to apoptosis stimulators (above, right). 

Structure analysis (including CD)  then determined that the impaired binding was caused by an altered conformation of the IAP protein.  Analysis of published IAP structures revealed that the conserved Arg makes several critical interactions (bridging hydrogen bonds, cation-p, helix-capping) that stabilize the IAP tertiary structure.  No other amino acid can make this same set of interactions.  Since the Arg resides on a face of the IAP opposite to where stimulators bind, it may be important for allosterically coupling stimulator binding to other IAP functions. 

Other studies are investigating the mechanism for how IAPs regulate the enzymatic activity of caspases.  One assay measures caspase activity by the increased fluorescence when the capase cleaves a synthetic substrate mimic. 

The information gained from these studies is providing detailed insight into how these proteins regulate apoptosis  in living cells.  It should also aid in developing therapies to treat diseases where apoptosis dysfunction occurs, such as cancer and neurodegeneration.